Databases

Recognizing that both the confidentiality of personal information and the openness of science are equally important, RIKEN IMS will continue to work in cooperation with other organizations in considering how best to release data that will contribute to human health and the conquest of disease.

• RIKEN IMS Basic Policy Regarding the Sharing of Human Genome Data

• List of analyzed human genome data the IMS has published and registered

  List of human genome data or summary statistics that IMS published

• Reference Database of Immune Cells (RefDIC)

  An open-access database of quantitative mRNA and protein profiles specifically for immune cells and tissues

  

• ZENBU

  A collaborative, omics data integration and interactive visualization system

  

• FANTOM

  Portal site for various databases built by the FANTOM project

  

• refTSS

  Reference data set of transcriptoin start sites in human and mouse

• SCPortalen

  A cell-centric single-cell RNA-seq data repository leveraging cutting-edge QC techniques and primary processing

Software

• MENTR

  A machine-learning model which reliably links genome sequence and ncRNA expression at the cell type level

• MOPLINE

  Short A computational algorithm (MOPline) that includes missing call recovery combined with high-confidence SV call selection and genotyping using short-read whole genome sequencing (WGS) data

• scDeepInsight

  A computational tool for analyzing single-cell RNA-seq data to identify cell types

• DeepInsight-3D

  A computational tool for predicting response to anticancer drugs using multi-omics and deep learning

• DeepFeature

  Short A computational tool for extracting features from non-image data, such as genes, using deep learning

• DeepInsight

  A computational analysis tool to transform non-image data such as genes for deep learning

Protocol

• CAGE

  A method for genome-wide identification of transcription start sites

• SINEUPs

  A new class of translation regulating RNA

• Publicly open databases, software and protocols contributed by RIKEN IMS researchers (Summary)